New age of open science




  • “Open Science” = umbrella term encompassing everything related to reproducible, transparent science.
    • reproducible science =


  • Movement to make all scientific data, methods, and materials accessible to all levels of society


  • Appeals to every area of science, from life sciences to computational sciences to theoretical sciences.

Why is ‘Open Science’ a good thing?




  • The vast majority of research is publicly funded
    • logical that the public have access to it!


  • Open and transparent research makes peer review and replication much easier





  • There is evidence that Open Science gives projects more downstream impact in the scientific community
    • question - how would this concept work with cancer research?

Major themes that comprise ‘Open Science’ guidelines


Open data: all data used in the project should be made available.


Open source: all code written in the project should be publicly available.


Open methods: the exact procedure of the project is publicly documented.


Open review: correspondence between reviewers and authors is public.


Open access: resulting publications are publicly available.


Open education: all education materials are publicly available

Open data is the core of ‘Open Science’


  • Publish all of the data used in your study and experiments online.


  • Definite shift from prior precedent
    • most raw data from scientific experiments not available


  • Many repositories and online data banks now exist
    • authors still given credit (DOI)
    • Many research institutions/companies host their own open data repositories


Brainstorm: Are there any issues with ‘Open Science’?

Can you use these data for your capstone: YES!!!



  • Explore data portals based on your career interest
    • ecological → health care


  • Propose a scientific question


  • Make sure that the data is not published
    • if it is, use in review-type paper


  • Work with Dr. C to download data
    • data sets can be really big

National Ecological Observation Network (NEON)


  • Offers ecological data from sites across the continent to fuel current ecological science


  • NEON is a network of field research sites, designed by ecologists to provide open data for all
    • 81 field sites across the U.S.
    • fully operational in 2019


  • NEON monitors ecosystems across the United States
    • freshwater = streams, rivers and lakes
    • terrestrial = deserts → tropical forests


  • Data is free to use!!

https://www.neonscience.org/data

NEON takes millions of measurements and collects thousands of samples every year

Lots of medical, human population and public health databases



  • Center of Disease Control (CDC)
    • public health data


  • 1000 Genomes project


  • Data.gov


  • World Health Organization (WHO)


  • SEER

CDC Wonder


  • An integrated information and communication system for public health by the CDC
    • promote information-driven decision making by placing timely, useful facts in the hands of public health practitioners and researchers
    • To provide the general public with access to specific and detailed information from CDC.



Wide-ranging data portal for epidemiologic research


Access to a wide array of public health information

https://wonder.cdc.gov/

1000 Genomes Project




  • Detailed catalogs of human genetic variation


  • Sequenced more than 2500 individuals from 26 different populations around the world


  • Integrated set of phased haplotypes with more than 80 million variants for these individuals
    • group of genes within an organism that was inherited together from a single parent

https://www.internationalgenome.org/data-portal/sample

Data.gov


  • Home of the U.S. Government’s open data
    • over 300,000 data sets
    • includes a broad coverage of science data


  • Data, accountability, and transparency: creating a data strategy and infrastructure for the future


  • Federal Data Strategy (FDS) encompasses a 10-year vision for how the Federal Government will accelerate the use of data to deliver on mission, serve the public, and steward resources while protecting security, privacy, and confidentiality.

https://labs.data.gov/dashboard/offices/qa

World Health Organization (WHO)

  • Founded in 1948, WHO is the United Nations agency that connects nations, partners and people to promote health, keep the world safe and serve the vulnerable


  • WHO manages and maintains a wide range of data collections related to global health


  • WHO has several global missions:
    • leads global efforts to expand universal health coverage
    • direct and coordinate the world’s response to health emergencies
    • promote healthier lives – from pregnancy through old age


  • The Global Health Observatory (GHO) data repository is WHO’s portal to health-related statistics
    • provides access to over 1000 health topics indicators
    • many available to download

https://www.who.int/data

Workshop Assignment: Exploring open data portals




  • Download the assignment worksheet from Brightspace


  • Using the available data portals from WHO, explore data trends and collaboratively propose questions that can only be answered with large open data sets
    • focus on the Triple Billion Targets or the Covid-19 Dashboard


  • Work in collaborative teams up to 3 people
    • submit your own work